SAXSdb — 7c8i

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase

Bifidobacterium longum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	PHOSPHOENOLPYRUVATE × 8 THIAMINE DIPHOSPHATE × 8 CALCIUM ION × 8 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6R2Q7_BIFLN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–825； UniProt 1–825 Author chain B； PDBConstruct 1–825； UniProt 1–825 Author chain C； PDBConstruct 1–825； UniProt 1–825 Author chain D； PDBConstruct 1–825； UniProt 1–825 Author chain E； PDBConstruct 1–825； UniProt 1–825 Author chain F； PDBConstruct 1–825； UniProt 1–825 Author chain G； PDBConstruct 1–825； UniProt 1–825 Author chain H； PDBConstruct 1–825； UniProt 1–825

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7c8i
Deposition date deposition_date	2020-06-01
Structure title title	Ambient temperature structure of Bifidobacgterium longum phosphoketolase with thiamine diphosphate and phosphoenol pyuruvate
Keywords keywords	;XFEL-SFX, ambient temperature, aldehyde-lyase activity, carbohydrate metabolic process, thiamine-diphosphate (ThDpp), phosphoenol pyuruvate (PEP), LYASE ;; LYASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

7c8i__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7c8i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7c8i__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	61.87 Å
Rg (electron density)	61.30 Å
Total Rg	61.41 Å
Atom count	51713
Residues	6465
Excluded volume	909080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7c8i__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase
Molecular weight formula_weight	93450.0 kDa
EC 编号 ec_number	4.1.2.22
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	52775

MTSPVIGTPWKKLNAPVSEEALEGVDKYWRVANYLSIGQIYLRSNPLMKEPFTREDVKHRLVGHWGTTPGLNFLIGHINRFIADHGQNTVIIMGPGHGGPAGTSQSYLDGTYTETFPKITKDEAGLQKFFRQFSYPGGIPSHFAPETPGSIHEGGELGYALSHAYGAIMDNPSLFVPAIVGDGEAETGPLATGWQSNKLVNPRTDGIVLPILHLNGYKIANPTILSRISDEELHEFFHGMGYEPYEFVAGFDDEDHMSIHRRFAELWETIWDEICDIKATAQTDNVHRPFYPMLIFRTPKGWTCPKYIDGKKTEGSWRSHQVPLASARDTEAHFEVLKNWLESYKPEELFDANGAVKDDVLAFMPKGELRIGANPNANGGVIRNDLKLPNLEDYEVKEVAEYGHGWGQLEATRTLGAYTRDIIKNNPRDFRIFGPDETASNRLQASYEVTNKQWDAGYISDEVDEHMHVSGQVVEQLSEHQMEGFLEAYLLTGRHGIWSSYESFVHVIDSMLNQHAKWLEATVREIPWRKPIASMNLLVSSHVWRQDHNGFSHQDPGVTSVLLNKCFHNDHVIGIYFATDANMLLAIAEKCYKSTNKINAIIAGKQPAATWLTLDEARAELEKGAAAWDWASTAKNNDEAEVVLAAAGDVPTQEIMAASDKLKELGVKFKVVNVADLLSLQSAKENDEALTDEEFADIFTADKPVLFAYHSYAHDVRGLIYDRPNHDNFNVHGYEEEGSTTTPYDMVRVNRIDRYELTAEALRMIDADKYADKIDELEKFRDEAFQFAVDNGYDHPDYTDWVYSGVNTDKKGAVTATAATAGDNEHHHHHH

Source Source

Source organism organism	Bifidobacterium longum
NCBI taxonomy ID ncbi_taxonomy_id	216816
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PHOSPHOENOLPYRUVATE
Molecular weight formula_weight	168.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	THIAMINE DIPHOSPHATE
Molecular weight formula_weight	425.3 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1022

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Unit-cell length a length_a	145.300 Å
Unit-cell length b length_b	184.940 Å
Unit-cell length c length_c	163.130 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	48.100 Å
R factor r_factor	0.1690
R_work r_work	0.1661
R_free r_free	0.2257

Ambient temperature structure of Bifidobacgterium longum phosphoketolase with thiamine diphosphate and phosphoenol pyuruvate

1. Protein Identity and Related Structures Protein Identity & Related Structures

Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7c8i__assembly_1__model_1

7c8i__assembly_1__model_1 | I(q)

7c8i__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Ambient temperature structure of Bifidobacgterium longum phosphoketolase with thiamine diphosphate and phosphoenol pyuruvate

1. Protein Identity and Related Structures Protein Identity & Related Structures

Xylulose-5-phosphate/fructose-6-phosphate phosphoketolase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7c8i__assembly_1__model_1

7c8i__assembly_1__model_1 | I(q)

7c8i__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)